| name | bioconductor-keggrest |
| description | A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST |
| when_to_use | Use when: Exploring available KEGG databases and organisms using listDatabases() and keggList().; Retrieving specific KEGG entries, including amino acid (aaseq) or nucleotide (ntseq) sequences as AAStringSet or DNAStringSet objects using keggGet().; Downloading KEGG pathway maps as PNG images using keggGet() with the "image" option.; Searching for genes or compounds by keywords, chemical formulas, or exact . Not for: For commercial applications, use ReactomePA instead because the KEGG API is strictly restricted to academic use by academic institutions.; For offline or high-throughput batch queries of thousands of genes, use local annotation packages like org.Hs.e |
| user-invocable | false |
KEGGREST
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.52.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Imports: httr, png, Biostrings
- Install:
BiocManager::install("KEGGREST")
When to Use
- Exploring available KEGG databases and organisms using
listDatabases() and keggList().
- Retrieving specific KEGG entries, including amino acid (
aaseq) or nucleotide (ntseq) sequences as AAStringSet or DNAStringSet objects using keggGet().
- Downloading KEGG pathway maps as PNG images using
keggGet() with the "image" option.
- Searching for genes or compounds by keywords, chemical formulas, or exact mass using
keggFind().
- Converting between KEGG identifiers and external database IDs (e.g., NCBI Gene ID) using
keggConv().
When NOT to Use
- For commercial applications, use
ReactomePA instead because the KEGG API is strictly restricted to academic use by academic institutions.
- For offline or high-throughput batch queries of thousands of genes, use local annotation packages like
org.Hs.eg.db instead to avoid server-side limitations.
- For complex pathway network topology analyses, use
KEGGgraph or ROntoTools instead.
Data Requirements
- Valid Identifiers: Input queries must be valid KEGG identifiers (e.g.,
"hsa:10458", "path:hsa00010", "cpd:C00493") or supported external identifiers.
- Internet Connection: An active internet connection is required to query the live KEGG REST API.
Key Parameters
- database: The target KEGG database to query (e.g.,
"pathway", "organism", "compound", "genes").
- query: The search term, identifier, or vector of identifiers to retrieve (e.g.,
"hsa:10458").
- option: Specific query options for
keggGet() (e.g., "aaseq", "ntseq", "image") or keggFind() (e.g., "formula", "exact_mass", "mol_weight").
Best Practices
- Verify the target organism's official KEGG code (e.g.,
"hsa" for human, "eco" for E. coli) using keggList("organism") before running queries.
- Limit
keggGet() queries to a maximum of 10 identifiers at once, as the server restricts larger batches.
- Use
keggLink() to find relationships across databases, such as retrieving all pathways associated with specific genes.
Common Pitfalls
- Truncated results from keggGet(): Occurs when supplying more than 10 inputs to
keggGet(); fix this by batching requests into chunks of 10 or fewer.
- Invalid organism code: Using common names instead of the official 3-4 letter KEGG code returns empty results; fix this by looking up the code with
keggList("organism").
- Commercial use violation: Occurs when using the package for non-academic purposes; fix this by switching to open-source databases like Reactome.
Alternatives
ReactomePA: For pathway analysis using the open-source, commercially unrestricted Reactome database.clusterProfiler: For comprehensive enrichment analysis integrating KEGG and GO annotations locally.AnnotationDbi: For local, offline mapping of gene IDs without relying on web APIs.
Citations
- Tenenbaum D (2024). KEGGREST: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG). R package version 1.46.0.
- Kanehisa M, Goto S (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1), 27-30.
References
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